CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	PknotsRG		TurboFold(seed)
MCC	0.592	>	0.517
Average MCC ± 95% Confidence Intervals	0.635 ± 0.200	>	0.510 ± 0.236
Sensitivity	0.517	>	0.422
Positive Predictive Value	0.683	>	0.642
Total TP	136	>	111
Total TN	33361	<	33387
Total FP	73	>	72
Total FP CONTRA	11	>	8
Total FP INCONS	52	<	54
Total FP COMP	10	=	10
Total FN	127	<	152
P-value	0.0

Comparison of performance of PknotsRG and TurboFold(seed). Positive Predictive Value (PPV) is plotted against sensitivity. Each dot represents a single test of each method. See tables below for raw data (individual counts for PknotsRG and TurboFold(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for PknotsRG and TurboFold(seed). The whiskers correspond to 95% confidence intervals (CIs). 'n' denotes the number of MCCs used to calculate average MCCs and CIs. See tables below for raw data (individual counts for PknotsRG and TurboFold(seed)).

Total Scores
MCC	0.592
Average MCC ± 95% Confidence Intervals	0.635 ± 0.200
Sensitivity	0.517
Positive Predictive Value	0.683
Nr of predictions	8

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LC8_A	GP_knot1 links to Rfam database...	0.63	0.55	0.73	11	1525	4	1	3	0	9
3RKF_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2191	0	0	0	0	14
3SD1_A	THF links to Rfam database...	0.61	0.50	0.75	21	3888	7	1	6	0	21
4A1C_2	5_8S_rRNA links to Rfam database...	0.14	0.15	0.13	5	11742	43	5	29	9	28
4A1C_3	5S_rRNA links to Rfam database...	0.70	0.59	0.82	32	7101	7	1	6	0	22
4AOB_A	SAM links to Rfam database...	0.50	0.40	0.63	17	4344	11	2	8	1	25
4ENB_A	crcB links to Rfam database...	0.89	0.79	1.00	15	1260	0	0	0	0	4
4ENC_A	crcB links to Rfam database...	0.86	0.79	0.94	15	1310	1	1	0	0	4

Total Scores
MCC	0.517
Average MCC ± 95% Confidence Intervals	0.510 ± 0.236
Sensitivity	0.422
Positive Predictive Value	0.642
Nr of predictions	8

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LC8_A	GP_knot1 links to Rfam database...	-0.01	0.00	0.00	0	1525	15	2	13	0	20
3RKF_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2191	0	0	0	0	14
3SD1_A	THF links to Rfam database...	0.59	0.48	0.74	20	3889	7	1	6	0	22
4A1C_2	5_8S_rRNA links to Rfam database...	0.15	0.15	0.15	5	11748	37	3	25	9	28
4A1C_3	5S_rRNA links to Rfam database...	0.69	0.57	0.84	31	7103	6	0	6	0	23
4AOB_A	SAM links to Rfam database...	0.56	0.40	0.77	17	4349	6	1	4	1	25
4ENB_A	crcB links to Rfam database...	0.69	0.47	1.00	9	1266	0	0	0	0	10
4ENC_A	crcB links to Rfam database...	0.65	0.47	0.90	9	1316	1	1	0	0	10

Matthews Correlation Coeffient, Sensitivity and Positive Predictive Value have been calculated based on the paper by Gardener & Giegerich, 2004.